Supplementary Information : Hogan, Holland, Holloway, Petit and Read : Read Classification for Next Generation Sequencing, ESANN 2013, April 2013

This item provides supplementary materials for the paper mentioned in the title, specifically a range of organisms used in the study. The full abstract for the main paper is as follows: Next Generation Sequencing (NGS) technologies have revolutionised molecular biology, allowing clinical sequencing to become a matter of routine. NGS data sets consist of short sequence reads obtained from the machine, given context and meaning through downstream assembly and annotation. For these techniques to operate successfully, the collected reads must be consistent with the assumed species or species group, and not corrupted in some way. The common bacterium Staphylococcus aureus may cause severe and life-threatening infections in humans,with some strains exhibiting antibiotic resistance. In this paper, we apply an SVM classifier to the important problem of distinguishing S. aureus sequencing projects from alternative pathogens, including closely related Staphylococci. Using a sequence k-mer representation, we achieve precision and recall above 95%, implicating features with important functional associations.

A lightweight biometric signature scheme for user authentication over networks

We introduce a lightweight biometric solution for user authentication over networks using online handwritten signatures. The algorithm proposed is based on a modified Hausdorff distance and has favorable characteristics such as low computational cost and minimal training requirements. Furthermore, we investigate an information theoretic model for capacity and performance analysis for biometric authentication which brings additional theoretical insights to the problem. A fully functional proof-of-concept prototype that relies on commonly available off-the-shelf hardware is developed as a client-server system that supports Web services. Initial experimental results show that the algorithm performs well despite its low computational requirements and is resilient against over-the-shoulder attacks.

Classification of railway bridges based on criticality and vulnerability factors

Bridges are currently rated individually for maintenance and repair action according to the structural conditions of their elements. Dealing with thousands of bridges and the many factors that cause deterioration, makes this rating process extremely complicated. The current simplified but practical methods are not accurate enough. On the other hand, the sophisticated, more accurate methods are only used for a single or particular bridge type. It is therefore necessary to develop a practical and accurate rating system for a network of bridges. The first most important step in achieving this aim is to classify bridges based on the differences in nature and the unique characteristics of the critical factors and the relationship between them, for a network of bridges. Critical factors and vulnerable elements will be identified and placed in different categories. This classification method will be used to develop a new practical rating method for a network of railway bridges based on criticality and vulnerability analysis. This rating system will be more accurate and economical as well as improve the safety and serviceability of railway bridges.

The cost of carbon : capital market effects of the proposed emission trading scheme (ETS)

In March 2008, the Australian Government announced its intention to introduce a national Emissions Trading Scheme (ETS), now expected to start in 2015. This impending development provides an ideal setting to investigate the impact an ETS in Australia will have on the market valuation of Australian Securities Exchange (ASX) firms. This is the first empirical study into the pricing effects of the ETS in Australia. Primarily, we hypothesize that firm value will be negatively related to a firm's carbon intensity profile. That is, there will be a greater impact on firm value for high carbon emitters in the period prior (2007) to the introduction of the ETS, whether for reasons relating to the existence of unbooked liabilities associated with future compliance and/or abatement costs, or for reasons relating to reduced future earnings. Using a sample of 58 Australian listed firms (constrained by the current availability of emissions data) which comprise larger, more profitable and less risky listed Australian firms, we first undertake an event study focusing on five distinct information events argued to impact the probability of the proposed ETS being enacted. Here, we find direct evidence that the capital market is indeed pricing the proposed ETS. Second, using a modified version of the Ohlson (1995) valuation model, we undertake a valuation analysis designed not only to complement the event study results, but more importantly to provide insights into the capital market's assessment of the magnitude of the economic impact of the proposed ETS as reflected in market capitalization. Here, our results show that the market assesses the most carbon intensive sample firms a market value decrement relative to other sample firms of between 7% and 10% of market capitalization. Further, based on the carbon emission profile of the sample firms we imply a ‘future carbon permit price’ of between AUD$17 per tonne and AUD$26 per tonne of carbon dioxide emitted. This study is more precise than industry reports, which set a carbon price of between AUD$15 to AUD$74 per tonne.

An accurate numerical scheme for the contraction of a bubble in a Hele-Shaw cell

We report on an accurate numerical scheme for the evolution of an inviscid bubble in radial Hele-Shaw flow, where the nonlinear boundary effects of surface tension and kinetic undercooling are included on the bubble-fluid interface. As well as demonstrating the onset of the Saffman-Taylor instability for growing bubbles, the numerical method is used to show the effect of the boundary conditions on the separation (pinch-off) of a contracting bubble into multiple bubbles, and the existence of multiple possible asymptotic bubble shapes in the extinction limit. The numerical scheme also allows for the accurate computation of bubbles which pinch off very close to the theoretical extinction time, raising the possibility of computing solutions for the evolution of bubbles with non-generic extinction behaviour.

The Stitchery collective : fashion in an expanded field

This practice-based presentation explores the role of fashion as an agent for social inclusion and ethical design practice in communities. The Stitchery Collective is an artist-run initiative based in Brisbane, Australia. Operating at the intersection of craft and design, the fashion-based initiative challenges the assumption that fashion is designed, produced and consumed exclusively in the commercial sector. As a not-for-profit cooperative, the stitchery collective is the first and only fashion organisation in Australia to attract funding under the national and state artist-run-initiative scheme. The collective approach extends to the stitchery design practice, facilitated by individual practitioners working within the organisation who devise programs in the context of collaborative and socially engaged design. Working under the banner of a question, Can fashion be more than pretty clothes for pretty people? the stitchery works to extend the cultural field of fashion practice in the 21st century. The premise of dress as a ‘significant creative or cultural expression’ has informed the expanded definition of fashion practice, as adopted by the stitchery. This alternative classification has fostered partnerships with numerous community groups, including those marginalised in the contemporary fashion context such as recent migrants and refugees. Community engagement programs span design, sewing and up-cycling workshops, sustainability lectures, clothing swaps and public education seminars, supported by partnerships with various cultural, government and educational institutions. In 2011, the stitchery travelled to the Venice Biennale’s 3rd International Children’s Carnival, hosting a workshop series and installation to promote design for sustainability. The proven potential for design to connect community members has motivated the stitchery to question the opportunity for fashion practice to, perhaps uncharacteristically, operate under the banner of ‘design for social good’. Acknowledging craft and design as relational fields, this presentation expands fashion as a tool for social innovation and sustainable practice. The stitchery dislocates the consumer status of fashion with small-scale, localised projects; moving beyond fashion as a dictum of social class to an alternative model that is accessible, conscious, flexible, connected and sustainable. As an undefined post-industrial future approaches, the non-commercial status of the stitchery practice might work to present an image of the active post-consumer. How can the stitchery propose a resilient model of design for the future?

A Flight control scheme to improve position tracking performance of rotary-wing UASs

This paper outlines an innovative and feasible flight control scheme for a rotary-wing unmanned aerial system (RUAS) with guaranteed safety and reliable flight quality in a gusty environment. The proposed control methodology aims to increase gust-attenuation capability of a RUAS to ensure improved flight performance when strong gusts occur. Based on the design of an effective estimator, an altitude controller is firstly constructed to synchronously compensate for fluctuations of the main rotor thrust which might lead to crashes in a gusty environment. Afterwards, a nonlinear state feedback controller is proposed to stabilize horizontal positions of the RUAS with gust-attenuation property. Performance of the proposed control framework is evaluated using parameters of a Vario XLC helicopter and high-fidelity simulations show that the proposed controllers can effectively reduce side-effect of gusts and demonstrate performance improvement when compared with the proportional-integral-derivative (PID) controllers.

Read classification for next generation sequencing

Next Generation Sequencing (NGS) has revolutionised molec- ular biology, allowing routine clinical sequencing. NGS data consists of short sequence reads, given context through downstream assembly and annotation, a process requiring reads consistent with the assumed species or species group. The common bacterium Staphylococcus aureus may cause severe and life-threatening infections in humans, with some strains exhibiting antibiotic resistance. Here we apply an SVM classifier to the important problem of distinguishing S. aureus sequencing projects from other pathogens, including closely related Staphylococci. Using a sequence k-mer representation, we achieve precision and recall above 95%, implicating features with important functional associations.

Key derivation function : the SCKDF scheme

A key derivation function is used to generate one or more cryptographic keys from a private (secret) input value. This paper proposes a new method for constructing a generic stream cipher based key derivation function. We show that our proposed key derivation function based on stream ciphers is secure if the underlying stream cipher is secure. We simulate instances of this stream cipher based key derivation function using three eStream finalist: Trivium, Sosemanuk and Rabbit. The simulation results show these stream cipher based key derivation functions offer efficiency advantages over the more commonly used key derivation functions based on block ciphers and hash functions.

Cardiomyopathy classification : ongoing debate in the genomics era

Cardiomyopathies represent a group of diseases of the myocardium of the heart and include diseases both primarily of the cardiac muscle and systemic diseases leading to adverse effects on the heart muscle size, shape, and function. Traditionally cardiomyopathies were defined according to phenotypical appearance. Now, as our understanding of the pathophysiology of the different entities classified under each of the different phenotypes improves and our knowledge of the molecular and genetic basis for these entities progresses, the traditional classifications seem oversimplistic and do not reflect current understanding of this myriad of diseases and disease processes. Although our knowledge of the exact basis of many of the disease processes of cardiomyopathies is still in its infancy, it is important to have a classification system that has the ability to incorporate the coming tide of molecular and genetic information. This paper discusses how the traditional classification of cardiomyopathies based on morphology has evolved due to rapid advances in our understanding of the genetic and molecular basis for many of these clinical entities.

Separable and non-separable discrete wavelet transform based texture features and image classification of breast thermograms

Highly sensitive infrared cameras can produce high-resolution diagnostic images of the temperature and vascular changes of breasts. Wavelet transform based features are suitable in extracting the texture difference information of these images due to their scale-space decomposition. The objective of this study is to investigate the potential of extracted features in differentiating between breast lesions by comparing the two corresponding pectoral regions of two breast thermograms. The pectoral regions of breastsare important because near 50% of all breast cancer is located in this region. In this study, the pectoral region of the left breast is selected. Then the corresponding pectoral region of the right breast is identified. Texture features based on the first and the second sets of statistics are extracted from wavelet decomposed images of the pectoral regions of two breast thermograms. Principal component analysis is used to reduce dimension and an Adaboost classifier to evaluate classification performance. A number of different wavelet features are compared and it is shown that complex non-separable 2D discrete wavelet transform features perform better than their real separable counterparts.

Genus Umbravirus

The practical need to partition the world of viruses into distinguishable, universally agreed upon entities is the ultimate justification for developing a virus classification system. The Author of this Book is Andrew MQ King, Elliot Lefkowitz, Eric B. Carstens, Michael J. Adams Since 1971, the International Committee on Taxonomy of Viruses (ICTV) operating on behalf of the world community of virologists has taken on the task of developing a single, universal taxonomic scheme for all viruses infecting animals (vertebrate, invertebrates, and protozoa), plants (higher plants and algae), fungi, bacteria, and archaea.

A flexible protection scheme for an islanded Multi-Microgrid

Multi-Microgrids (MMGs) have been proposed to connect distributed generators (DG), microgrids (MG), and medium-voltage (MV) loads with the distribution system. A flexible protection scheme that enables an islanded MMG to continue operation during fault conditions is yet to be developed. In this paper, a protection scheme for an islanded MMG that utilises MG controllers and communication links is proposed. The MMG model used includes two MGs connected to the distribution system. Each MG consists of diesel, wind, and photovoltaic (PV) microsources. The effectiveness of the proposed protection scheme is evaluated by simulation.

A novel real time pricing scheme for demand response in residential distribution systems

Price based technique is one way to handle increase in peak demand and deal with voltage violations in residential distribution systems. This paper proposes an improved real time pricing scheme for residential customers with demand response option. Smart meters and in-home display units are used to broadcast the price and appropriate load adjustment signals. Customers are given an opportunity to respond to the signals and adjust the loads. This scheme helps distribution companies to deal with overloading problems and voltage issues in a more efficient way. Also, variations in wholesale electricity prices are passed on to electricity customers to take collective measure to reduce network peak demand. It is ensured that both customers and utility are benefitted by this scheme.